1. Wei Zhao, Meng Xu, Zhi Liang, Bo Ding, Liwen Niu, Haiyan Liu*, and Maikun Teng*, Structure-based de novo prediction of zinc-binding sites in proteins of unknown function, Bioinformatics 2011 27: 1262-1268.
2. Jian Zhan, Bo Ding, Rui Ma, Xiaoyu Ma, Xiaofeng Su, Yun Zhao, Ziqing Liu, Jiarui Wu, Haiyan Liu*, Develop Reusable and Combinable Designs for Transcriptional Logic Gates, Mol Syst Biol 2010,6:388.
3. Quan Li, Changhai Zhou, Haiyan Liu*, Fragment-based local statistical potentials derived by combining an alphabet of protein local structures with secondary structures and solvent accessibilities. Proteins. 2009, 74, 820-36.
4. Zanxia Cao, Haiyan Liu*; Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides; J Chem Phys, 2008, 129, 015101.
5. Cao Xu, Jun Wang, Haiyan Liu*, A Hamiltonian replica exchange approach and its application to the study of side chain type and neighbor effects on peptide backbone conformations, J Chem Theor Comput, 2008,4,1348-1359.
6. Jun Wang, Yan Gu, Haiyan Liu*; Determination of conformational free energies of peptides by multidimensional adaptive umbrella sampling; J Chem Phys 2006,125, 094907.
7. Sanmei Cheng, Yuedong Yang, Wenrui Wang, Haiyan Liu*; Transition State Ensemble for the Folding of B Domain of Protein A: A Comparison of Distributed Molecular Dynamics Simulations with Experiments; J Phys Chem B. 2005,109, 23645-23654.
8. Li Xie, Haiyan Liu*, Yang Weitao*; Adapting the nudged elastic band method for determining minimum-energy paths of chemical reactions in enzymes, J Chem Phys, 2004, 120,8039.
9. Jiang Zhu, Qianqian Zhu, Yunyu Shi and Haiyan Liu*; How Good can we predict native contacts in proteins based on decoy structures and their energies? Proteins, 2003,52, 598.
10. Zhiyong Zhang, Yunyu Shi*, and Haiyan Liu*; Molecular dynamics simulations of peptides and proteins with amplified collective motions, Biophys J, 2003, 84, 3583.